This reports the protocol used to align the nonRice_MarkerRFLP features to Oryza_sativa_indica-chromosome-20070724.
Tue Aug  7 14:44:16 2007


Source of nonRice_MarkerRFLP : These are obtained from Cornell 

Alignment procedure details 
--------------------------- 

1897 nonRice_MarkerRFLP are aligned to Oryza_sativa_indica-chromosome-20070724 using blat with blat parameters -minIdentity=50 followed by PslReps with -singleHit. This was followed by a filtering procedure described below and applied in general to 'CrossSpecies-Coding' data sets.

Initial summary
# alignments : 160
# unique Features these alignments represent: 136
% of total features these alignments represent : 7.17 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 109
150	 21
200	 16
250	 5
300	 1
350	 0
400	 2
450	 5
500	 0
550	 0
600	 0
650	 1
700	 0
750	 0
800	 0
10000	 0

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 30
# unique Features these remaining alignments represent: 29
% of total features these alignments represent : 1.53 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 28
2	 1
3	 0
4	 0
5	 0
6	 0
8	 0
9	 0
10	 0
20	 0
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 30
# unique Features these remaining alignments represent: 29
% of total features these alignments represent : 1.53 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 0
40	 0
50	 0
60	 0
70	 0
80	 0
90	 0
95	 23
100	 7

Following is the distribution of gaps
Gaps	# features
--------	--------
1000	 25
2000	 3
3000	 0
4000	 0
5000	 0
6000	 0
7000	 0
8000	 0
9000	 0
10000	 0

Following is the final summary
# alignments : 30
# unique Features these alignments represent: 29
% of total features these alignments represent : 1.53 %
  

Last modified: Thu Sep 13 15:01:03 2007